Uses fecundity objects to construct a matrix defining per-capita contribution to recruitment stages (e.g., propagules [seed, spore], seedlings, calves) by reproductive stages due to sexual reproduction.
NOTE - old createIPMFmatrix is being deprecated; use makeIPMFmatrix instead.
numeric, number of environmental classes, always = 1 for
non-compound matrices.
nBigMatrix
numeric, number of size bins in the F matrix, defaults to 50.
minSize
numeric, minimum size of the F matrix, defaults to -1.
maxSize
numeric, maximum size of the F matrix, defaults to 50.
chosenCov
data-frame indicating level of the discrete covariate, or
range of values where multiple covariates are modeled.
integrateType
integration type, defaults to "midpoint" (which uses probability density
function); other option is "cumul" (which uses the cumulative density function)
correction
correction type, defaults to none. The first option is constant which will multiply every column of the IPM by a constant sufficient to adjust values to those predicted for total fertility at that size. The second option is discretizeExtremes which will place all transitions to sizes smaller than minSize into the smallest bin, and transitions to sizes larger than maxSize into the largest bin.
preCensus
logical (TRUE or FALSE), indicating whether the fecundity object should
represent an interval between pre-breeding or a post-breeding censusses.
defaults to TRUE (pre-breeding census), meaning that all reproduction
and offspring rates required for the F matrix are embedded in fecObj.
Alternatively, an F matrix based on post-breeding census (preCensus=FALSE)
requires additional survObj and growObj, to cover the survival and growth
of the parents until the reproduction event.
survObj
survival object, describing the survival of parents from a census until
the reproduction event starts (at some point during the inter-census time
step). If preCensus = FALSE but no survival object is provided, it is assumed
that all individuals survive to the breeding event.
growObj
growth object, describing the growth of parents that survive until the
reproduction event starts. Warning: this growth object is still ignored in
makeIPMFmatrix in the current version of IPMpack. It will become functional
in coming versions. So far it is assumed that at time of breeding the individuals
have the same size as at the beginning of the time interval.
offspringObj
growth object, describing the size of offspring (this process may alternatively appear in fecObj).
Value
an object of class IPMmatrix of dimensions nBigMatrix or nBigMatrix+nDiscrete classes (defined by fecObj@offspringSplitter-1).
Author(s)
C. Jessica E. Metcalf, Sean M. McMahon, Roberto Salguero-Gomez, Eelke Jongejans & Cory Merow.
References
For information on F matrix: Caswell. 2001. Matrix population models: construction, analysis, and interpretation. 2nd ed. Sinauer. p110-112.
For midpoint: Zuidema, Jongejans, Chien, During & Schieving. Integral projection models for trees: a new parameterization method and a validation of model output. Journal of Ecology 98, p345-355.
For multiple-vital rate integration on fecundity: Yang, Jongejans, Yang & Bishop. 2011. The effect of consumers and mutualists of Vaccinum membranaceum at Mount St. Helens: dependence on successional context. PLoS One 10, p1-11.
For information on unintentional eviction from IPMs (which the various corrections try and account for) see Williams et al. 2012 Avoiding unintentional eviction from integral projection models. Ecology.
See Also
makeIPMPmatrix,makeIPMCmatrix,makeIPMmatrix
Examples
# Data with only continuous stage and one habitat
dff <- generateData()
dff$fec[dff$fec==0] <- NA
fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log")
Fmatrix <- makeIPMFmatrix(fecObj = fv1, nBigMatrix = 20,
minSize = min(dff$size, na.rm = TRUE),
maxSize = max(dff$size, na.rm = TRUE), correction="constant")
slotNames(Fmatrix)
image(Fmatrix@meshpoints, Fmatrix@meshpoints, t(Fmatrix),
xlab = "Continuous (e.g. size) stage at t",
ylab = "Continous (e.g. size) stage at t+1")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(IPMpack)
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/IPMpack/makeIPMFmatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeIPMFmatrix
> ### Title: Builds F matrices.
> ### Aliases: makeIPMFmatrix createIPMFmatrix
>
> ### ** Examples
>
> # Data with only continuous stage and one habitat
> dff <- generateData()
> dff$fec[dff$fec==0] <- NA
> fv1 <- makeFecObj(dff, Formula = fec~size, Transform = "log")
> Fmatrix <- makeIPMFmatrix(fecObj = fv1, nBigMatrix = 20,
+ minSize = min(dff$size, na.rm = TRUE),
+ maxSize = max(dff$size, na.rm = TRUE), correction="constant")
>
> slotNames(Fmatrix)
[1] ".Data" "nDiscrete" "nEnvClass" "nBigMatrix"
[5] "meshpoints" "env.index" "names.discrete"
>
> image(Fmatrix@meshpoints, Fmatrix@meshpoints, t(Fmatrix),
+ xlab = "Continuous (e.g. size) stage at t",
+ ylab = "Continous (e.g. size) stage at t+1")
>
>
>
>
>
> dev.off()
null device
1
>